functional_enrichment-ConsensusPartition-method {cola} | R Documentation

## Perform functional enrichment on signature genes

### Description

Perform functional enrichment on signature genes

### Usage

    ## S4 method for signature 'ConsensusPartition'
    functional_enrichment(object, gene_fdr_cutoff = cola_opt$fdr_cutoff, k = suggest_best_k(object),
        row_km = NULL, id_mapping = guess_id_mapping(rownames(object), org_db, verbose),
        org_db = "org.Hs.eg.db", ontology = "BP",
        min_set_size = 10, max_set_size = 1000,
        verbose = TRUE, ...)

### Arguments

`object` | a `ConsensusPartition-class` object from `run_all_consensus_partition_methods`.
`gene_fdr_cutoff` | Cutoff of FDR to define significant signature genes.
`k` | Number of subgroups.
`row_km` | Number of row clusterings by k-means to separate the matrix that only contains signatures.
`id_mapping` | If the gene IDs which are row names of the original matrix are not Entrez IDs, a named vector should be provided where the names are the gene IDs in the matrix and values are correspoinding Entrez IDs. The value can also be a function that converts gene IDs.
`org_db` | Annotation database.
`ontology` | See corresponding argumnet in `functional_enrichment,ANY-method`.
`min_set_size` | The minimal size of the gene sets.
`max_set_size` | The maximal size of the gene sets.
`verbose` | Whether to print messages.
`...` | Pass to `functional_enrichment,ANY-method`.

### Details

For how to control the parameters of functional enrichment, see help page of `functional_enrichment,ANY-method`.

### Value

A list of data frames which correspond to results for the functional ontologies:

### Examples

    # There is no example
    NULL

[Package cola version 1.2.1 Index]